Abstract
Repetitive sequences account for a large proportion of the pear genome, suggesting that they play critical roles in the evolution of Pyrus. One form of repetitive sequences is transposable elements, which have been predominantly investigated thus far, including DNA transposons and retrotransposons. Approximately 22.5% of the ‘Bartlett’ genome (P. communis) and 42.4% of the ‘Suli’ genome (P. pyrifolia) are reported to be Long Terminal Repeat (LTR)-retrotransposons (LTR-RTs). Thus, investigation of transposable elements will offer new insights of the evolutionary history of Pyrus. LTR-RTs exhibit high heterogeneity and their copy numbers vary with the Pyrus species. The dynamics of LTR-RTs are an important source of genetic variation in Pyrus species. As of now, the function and development mechanism of transposable elements have not yet been fully understood. In this chapter, advances of transposable elements in Pyrus are presented and discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bailey L (1917) Standard cyclopedia of horticulture. Macmillan Press, New York, USA
Bergman CM, Quesneville H (2007) Discovering and detecting transposable elements in genome sequences. Brief Bioinform 8(6):382–392
Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24(3):1242–1255
Chagne D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knabel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VG, Schaffer RJ, Gardiner SE, Velasco R (2014) The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). Plos One 9(4):e92644
Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P, Quesneville H, Feuillet C, Choulet F (2014) Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biol 15(12):546
De Felice B, Wilson RR, Argenziano C, Kafantaris I, Conicella C (2009) A transcriptionally active copia-like retroelement in Citrus limon. Cell Mol Biol Lett 14(2):289–304
Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J (2010) Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63(4):584–598
El Baidouri M, Panaud O (2013) Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol Evol 5(5):954–965
Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3(5):329–341
Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20(14):3639–3644
Havecker ER, Gao X, Voytas DF (2004) The diversity of LTR retrotransposons. Genome Biol 5(6):225
Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation. Plant cell 12(3):357–369
Jiang S, Cai D, Sun Y, Teng Y (2016a) Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome. Mob DNA 7:1
Jiang S, Zheng X, Yu P, Yue X, Ahmed M, Cai D, Teng Y (2016b) Primitive genepools of asian pears and their complex hybrid origins inferred from fluorescent sequence-specific amplification polymorphism (SSAP) markers based on LTR retrotransposons. Plos One 11(2):e0149192
Jiang S, Zong Y, Yue X, Postman J, Teng Y, Cai D (2015) Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L. Mol Genet Genomic 290(1):225–237
Kalendar R, Flavell AJ, Ellis TH, Sjakste T, Moisy C, Schulman AH (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106(4):520–530
Kalendar R, Schulman AH (2006) IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc 1(5):2478–2484
Kim H, Terakami S, Nishitani C, Kurita K, Kanamori H, Katayose Y, Sawamura Y, Saito T, Yamamoto T (2012) Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear. Breed Sci 62(1):53–62
Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304(5673):982
Kuhn BC, Lopez-Ribera I, da Silva Machad MDEF, Vicient CM (2014) Genetic diversity of maize germplasm assessed by retrotransposon-based markers. Electrophoresis 35(12–13):1921–1927
Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33(1):479–532
Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14(5):860–869
Meyers BC, Tingley SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11(10):1660–1676
Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W Jr, Jordao H Jr, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AA, Vieira ML (2012) A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 13:51
Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002) Integration of cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12(5):795–807
Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16(10):1262–1269
Rubstov GA (1944) Geographical distribution of the genus Pyrus and trends and factors in its evolution. Am Nat 78:358–366
Sabot F, Schulman AH (2006) Parasitism and the retrotransposon life cycle in plants: a hitchhiker’s guide to the genome. Heredity 97(6):381–388
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20(1):43–45
SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274(5288):765–768
Shapiro JA (2005) Retrotransposons and regulatory suites. BioEssays 27(2):122–125
Smykal P, Bacova-Kerteszova N, Kalendar R, Corander J, Schulman AH, Pavelek M (2011) Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 122(7):1385–1397
Sun J, Hao Y, Li L, Song Y, Fan L, Zhang S, Wu J (2015) Evaluation of new irap markers of pear and their potential application in differentiating bud sports and other rosaceae species. Tree Genet Genomes 11(2):1–13
Teng Y, Tanabe K (2004) Reconsideration on the origin of cultivated pears native to East Asia. Acta Hortic 634:175–182
Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461(7262):423–426
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42(10):833–839
Verde I, Abbott AG, Scalabrin S, Jung S, Shu SQ, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan PF, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arus P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS, Initiative IPG (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487-U447
Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BB, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253(6):687–694
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8(12):973–982
Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23(2):396–408
Yin H, Du J, Wu J, Wei S, Xu Y, Tao S, Wu J, Zhang S (2015) Genome-wide annotation and comparative analysis of long terminal repeat retrotransposons between pear species of P. bretschneideri and P. communis. Sci Rep 5:17644
Yin H, Du JC, Li LT, Jin C, Fan L, Li M, Wu J, Zhang SL (2014) Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). Genome Biol Evol 6(6):1423–1436
Yin H, Wu X, Shi D, Chen Y, Qi K, Ma Z, Zhang S (2017) TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species. Mob DNA 8:14
Zheng X, Cai D, Potter D, Postmand J, Liu J, Teng Y (2014) Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences. Mol Phylogenet Evol 80:54–65
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Jiang, S., Teng, Y. (2019). Repetitive Sequences in Pear. In: Korban, S. (eds) The Pear Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-11048-2_8
Download citation
DOI: https://doi.org/10.1007/978-3-030-11048-2_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-11047-5
Online ISBN: 978-3-030-11048-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)